I don't think it's relevant, but I have a Flashforge Creator Pro 2016.

I've noticed an issue with the cooling fan setting with changing processes over layer height. If the cooling fan is set to the same settings for all layers (off until layer 3 when printing PLA, for example), the fan shuts off during the new process and come back on two layers later. This leads me to believe Simplify3D is treating the first layer in each process as "layer 0". However, setting the fan to On for layer 0 in the new process (which starts some ways up the part) results in the cooling fan turning on when the print begins (true layer 0). I've checked the g-code to make sure the cooling fan is doing what it is told, and the commands to turn it on and off at certain heights are definitely in there.

My work around for now is to delete the cooling fan settings for each new process beyond the base one to ensure the fan stays on after layer 3. This works, but it seems Simplify3D cannot save this information to the Factory file. Opening it back up auto adds "fan off at layer 0" to all processes that have no fan speeds defined, which seems to result in the fan never coming on at all.

This issue was causing a banding issue at the layer height where the processes changed.

I'm having this same problem with temperature control on multiple processes.

I currently have a topic on here about weird previews with multiple processes and as I've been troubleshooting it I've run into not being able to control my temperature correctly. I'm trying to do dual extrusion and keep one extruder fairly cool for most of the print and when the temp changes it changes back.

This originally started with my preview creating blank layers in the preview for the first process on any multiple process (it prints correctly though, or seems to) and now that I've done further testing, just a few hours ago I noticed it did the same thing with my temp settings as you describe with your fan settings.

Maybe that will help narrow the issue down because I'm running into a lot of issues now with dual extrusion printing.

Do you believe if I set all my temp settings in the first process and delete them all from subsequent processes that might work?

Edit: doesn't let me, requires at least one setpoint. If I try to give it a setpoint just for the layers that the process handles (such as layer 23 for the top of the print) it says it requires a setpoint for the start of the print as well

It's weird because the layer number in the process settings seems to want it both ways. That is, it treats layer 0 as the bed level (true first layer) but also subsequent layers are offset from the first process layer (potentially part way up the part). I can't say for sure the nozzle and bed temperatures follow the same logic as I haven't explored those.

All I can say is what I observe with the side cooling fan settings on a FFCP.

What I might try tonight, at least for the cooling fan, is to set the upper processes to turn the fan on at layer 3, with no information about layer 0. That way, even if the fan settings overlap from different processes, they all turn it on at the third layer. And if it sets the fan to on at the offset layer 3, the fan should already be on so there will be no change.